This GARNet research roundup includes papers that feature a number of different research areas. Firstly is work from Glasgow that investigates the photoactivation of the UVR8 light receptor. Second is work from the University of Cambridge that links the activity of the BIG protein to the circadian oscillator. The next paper has co-authors from Cambridge and looks at promotor sequences needed for expression in bundle sheath cells. The fourth paper from the University of Leeds documents an important role for peroxisomes in the drought response whilst the final manuscript includes co-authors from the University of Birmingham and looks at the role of the ASYNAPTIC4 protein during meiosis.

Aranzazu Díaz-Ramos and Andrew O’Hara are co-first authors on this research from the University of Glasgow that investigates the activation of photomorphogenic responses by the UVR8 photoreceptor. They show that two distinct UVR8 responses, either the monomerisation of UVR homodimers or accumulation of HY5 responsive transcripts, occurs at different wavelengths.

Timothy Hearn works with Alex Webb at the University of Cambridge and in this paper characterises how the multi-functional BIG protein impacts the circadian clock. This gene was isolated in a forward genetics screen to identify signaling components that alter the response to nicotinamide, which acts as a brake on the circadian oscillator. This finding allows the authors to better understand how altering the circadian oscillator can affect appropriate phasing during different environmental conditions.

Sandra Kirschner is first author on this German-led study that includes Helen Woodfield (now Cardiff University) and Julian Hibberd (University of Cambridge). They are interested in the mechanisms that restrict gene expression to bundle sheath cells in C3 plants with a longer view of understanding the biology of these cells in C4 plants. They analyse the vascular-restricted SULTR2;2 promotor and identified a short region that is necessary for its expression pattern. Importantly they show that this sequence is evolutionarily conserved across Brassicaceae and a distantly related C4 plant.

Heba Ebeed is the lead author of this work conducted in Alison Baker’s lab at the University of Leeds. They take a comparative genomics approach to investigate the expression of peroxisome-localised genes in a moss (physcomitrella), monocot (wheat) and a dicot (arabidopsis). They show that members of three gene families are upregulated in each of these organisms following drought stress, demonstrating the importance of peroxisomes in this environmental response throughout plant evolution.

Chris Franklin and Alice Darbyshire from the University of Birmingham are co-authors on this French-led study that looks into the role of the ASYNAPTIC4 (ASY4) protein in the control of synapsis formation during meiosis. Plants without ASY4 activity have defective chromosomal axis formation and cannot undergo synapsis. Although the initiation of recombination is unaffected in asy4 mutants, later processes are altered, demonstrating the key role for ASY4 during meiosis

The European Court GMO directive, published in 2001, makes it extremely challenging to have genetically modified (GM) crops approved for growth in EU member countries. The financial and time-costs required to develop these crop varieties mean that only one such crop, an insect resistant GM maize, is grown in small amounts in Spain. There is little doubt that the GMO Directive has stalled academic innovation and reduced external investment in crop breeding technology in the EU. Although opponents of the technology are pleased by the absence of Monsanto et al’s EU investment, the broader implication is that there is little use of this technology to generate crops that are resistant to biotic and abiotic stress or have improved nutritional qualities.

Over the past few years many parties have been awaiting a ruling from the European Court of Justice on the use of new breeding technologies, such as CRISPR-Cas9 gene editing, in the future development of crops. The case was brought to the ECJ by Confédération paysanne, which is a French agricultural union, who wanted a judgment on the use of crops generated by mutagenesis techniques.

Over a long period mutagenesis techniques have been used in conventional breeding to introduce 1000s of mutations into crop genomes in the hope of finding a beneficial alteration. However this ECJ case is really concerned with the use of gene editing technology, which has the ability to make precise targeted mutations in order to change gene function and subsequently plant phenotypes. Unlike with traditional GM, plants generated by gene editing techniques do not contain any trace of foreign genetic information, therefore leaving a crop that is indistinguishable from those generated by conventional mutagenesis. Importantly a GE crop can just have a single precise mutation whereas crops generated by conventional mutagenesis can have 1000s of unknown and uncharacterised mutations.

Plant scientists have been cautiously awaiting a positive verdict in this case after non-binding advice given in January by Michale Bobek the Advocate General that GE-induced mutagenesis should not be considered differently from conventional mutagenesis. This is also the opinion of US regulators who have set a much lower bar for approval of non-transgenic GE crops rather than GM crops.

However the ECJ draws back from a blanket ban of all mutagenesised crops as they state:

‘however, that it is apparent from the GMO Directive that it does not apply to organisms obtained by means of certain mutagenesis techniques, namely those which have conventionally been used in a number of applications and have a long safety record.

‘…the risks linked to the use of these new mutagenesis techniques might prove to be similar to those that result from the production and release of a GMO through transgenesis’.

This is ironic as there is a deep bank of evidence indicating that the risk posed by conventional GM crops is essentially zero, so the risk of GE crops could be similarly defined.

Unfortunately the GMO directive was written to respect the precautionary principle and has no consideration for this evidence. Therefore the reading of this statement sadly must be that GE crops pose some as yet unidentified danger to consumers and the environment.

Another unintentionally ironic statement from the ECJ ruling states…

‘and those new techniques make it possible to produce genetically modified varieties at a rate out of all proportion to those resulting from the application of conventional methods of mutagenesis’.

Yes this is true but not as the statement intended.

Indeed the use of GE technology will allow the generation of new crops much more rapidly than with conventional breeding. However the irony comes from the extremely targeted nature of GE technology as opposed to the 1000s of random mutations that are generated by conventional techniques.

For some unstated reason the ECJ considers that the rapid generation of new crop varieties is a negative consequence of this new technology even though there is no suggestion that any new varieties would not go through appropriate levels of regulation.

So what will be the effect of this ruling?

Unfortunately it will be a case of ‘as you were’ for both academics and biotech companies. Preparatory research will be conducted in growth rooms and glasshouses but at that stage there will be a blockage in what will be possible with any GE crop varieties. The UK government recently approved a field trial of both GM and GE crops but this is just an experimental plot with no suggestion that it is for general release.

Therefore the situation will remain the same with new advantageous crop varieties having nowhere to go in the EU after small field trials are concluded.

This blockage will undoubtedly stall scientific innovation in the EU as there will be little incentive for long-term investment if new crops varieties aren’t able to be used either for altruistic or financial gain. Innovation will continue in universities across Europe but any financial benefits will be gained by companies in the USA or elsewhere.

It’s a sad day for science, technology and evidence-based policy making across Europe.

With Brexit looming on the horizon is this a policy area in which the UK could set itself apart from the remainder of the EU?

Only time will tell but even if the UK does develop a more permissive regulatory environment, challenges will remain when moving GE-crops across EU borders.

This week’s GARNet research roundup begins with a set of papers looking at aspects of the plant defence response with a focus on the cell wall. Firstly work from Mike Deeks’ lab in Exeter assesses the role of FORMIN4 during pre-invasion cell wall apposition. Secondly Sara Pose and Paul Knox (Leeds) are involved with a study looking at how altered cell wall lignin composition alters the defense response. Finally Joe McKenna and Cyril Zipfel are co-authors on a Norwegian-led study that looks at the influence of plant cell wall integrity maintenance in immune signalling.

Relatedly is a study from the Devoto lab at RHUL looks at the role of the defence hormone methyl jasmonate in Arabidopsis cell culture.

Next are two papers that research different aspects of the plant ER. Verena Kriechbaumer (Oxford Brookes) looks at plant ER-localised Lunapark proteins whilst a study from the University of Warwick provides a preliminary structural analysis of the RTNLB13 reticulon protein.

The seventh and eight papers are involved with the plant response to different growth conditions. Research from University of Nottingham looks at the response of the cortical cell layer of the root meristem to low phosphate conditions whilst work from University of Southampton investigates the relationship between nitrate and copper signaling.

The next paper is from Emily Flashman’s lab at the University of Oxford and looks at the role of plant cysteine oxidases as oxygen sensors whilst the tenth paper features John Doonan (Aberystwyth University) as a co-author and investigates how a histone acetyltransferase affects trichome development.

Finally is a paper from Pierre Baudal and Kirsten Bomblies (John Innes Centre) that uses Arabidopsis arenosa as a model to investigate the emergence of novel flowering time alleles in populations that have colonised along railway corridors.

Stefan Sassmann is the lead author of this paper from Mike Deeks’s lab in Exeter. They investigate the role of the membrane-integrated FORMIN4 protein in the process of cell wall apposition, which occurs as part of the plant immune response and is dependent on actin dynamics. FORMIN4 is stably localised apart from the active traffic of the endomembrane system and removing its function compromises the defense response, presumably by altering actin distribution at sites of cell wall apposition. This work demonstrates that FORMIN4 acts as a key component of the pre-invasion defense response.

Sara Pose and Paul Knox (University of Leeds) are co-authors on this US-led study that investigates how lignin composition can influence the defence response. Plants with the same lignin content but changed lignin compositions show altered expression in genes involved with different arms of the defense response. This indicates that cell wall lignin composition plays a significant role in the plants ability to response to different sources of pathogen attack.

Joe McKenna (Imperial College, now Oxford Brookes University) and Cyril Zipfel (The Sainsbury Laboratory, Norwich) are co-authors on this Norwegian-led study that looks at the plant cell wall integrity maintenance mechanism and how it responses to the challenges of growth, development and environmental stresses. They identified a set of receptor-like kinases that are key for the responses elicted by cell wall damage (CWD). Conversely they showed that the components of the pattern-triggered immunity (PTI) signaling pathway repress responses to CWD. This study provides insights into how cell wall responses interact with downstream gene expression changes following pathogen challenge.

Moritz Bömer works with Alessandra Devoto at Royal Holloway University of London and leads this research that looks at the effect of MeJA treatment on growth and gene expression in Arabidopsis cell culture. They demonstrate that both MeJA treatment or COI1 overexpression causes changes in the abundance of proteins involved in cell wall loosening as well as altered levels of primary metabolites alanine, serine and succinic acid. This work demonstrates a close link between hormone signaling, the defence response and the metabolic profile of Arabidopsis cells.

Verena Kriechbaumer from Oxford Brookes University leads this research that investigates the in planta function of novel ER network-shaping proteins called Lunaparks (LNP). They show that these proteins localise to the entire ER network in Arabidopsis. They use confocal microscopy to show that altering the level of LNP gene expression changes ER morphology, possibly by regulating the formation of ER cisternae.

Michael Chow worked with Lorenzo Frigerio and Ann Dixon at the University of Warwick to provide a preliminary structure and topology analysis of the plant RTNLB13 reticulon protein. This ER-associated integral membrane protein was expressed in bacteria and then a variety of analysis techniques were used to suggest that RTNLB13 has a high level of self-association and protein-membrane interactions.

George Janes works with Anthony Bishopp at the University of Nottingham and leads this study that looks at root meristem development under low phosphate conditions. They show that in phosphate-limiting conditions the cortex layer of the root meristem contains almost double the number of cells, which results in a greater number of root hair-forming epidermal cells. As this change can occur within 24hrs the rapidity of the response represents a significant adaptation to a changing root environment.

Franz Hippler (University of Southampton) leads this UK-Brazil collaboration showing that growth of Arabidopsis plants in excess copper conditions causes a downregulation in nitrate uptake. This is due to both direct and indirect changes on the gene expression of nitrate transporters as well as a reduction in transcript level of the plasma membrane proton pump, AHA2. This effect was altered when copper levels were reduced demonstrating that copper toxicity acts at the level of nitrate transport and homeostasis.

Mark White is the lead author on this work from the lab of Emily Flashman at the University of Oxford in which they look at the role of plant cysteine oxidases (PCOs) as oxygen sensors. They assessed the kinetics of each of AtPCO1 to AtPCO5 proteins and show that the most catalytically competent isoform is AtPCO4, in terms of both responding to O2, and oxidizing hypoxic responsive proteins. This work validates an O2-sensing role for the PCOs and provides evidence for functional differences between members of this enzyme family.

John Doonan (Aberystwyth University) is a co-author on this manuscript led by Jenna Kotak and Amy Herd in the USA. They investigate plants that have mutations in the histone acetyltransferase GCN5 and associated transcriptional coactivator ADA2b. These genes have been previously demonstrated as being involved in endoreduplication and trichome branching. They show that these mutants have alterations in the number and patterning of trichome-branches and that ADA2b and GCN5 are required to couple nuclear content with cell growth and morphogenesis.

Pierre Baduel and Kirsten Bomblies (John Innes Centre) lead this work that was conducted prior to Kirsten’s move to Norwich. In this study they follow the colonization of populations of Arabidopsis arenosa along mountain railway corridors. They demonstrate that selective pressure has occurred on novel alleles of flowering time genes and discuss the implications for ruderal communities linked to railways as allele conduits linked to local adaptations.

This bumper GARNet Research Roundup begins with two sets of papers in related areas. First are three papers that investigate the biology of plasmodesmatata. These include work from the Faulkner lab at the JIC, the Band lab at Nottingham and a broad European collaboration that includes co-authors from Durham, Cambridge and St Andrews. The second[…]

Naresh Loudya from Royal Holloway University of London discusses a recent paper published in the Philosophical Transactions of the Royal Society B entitled ‘Retrograde signalling in a virescent mutant triggers an anterograde delay of chloroplast biogenesis that requires GUN1 and is essential for survival‘. Apologies for the high background noise early in the recording. http://blog.garnetcommunity.org.uk/wp-content/uploads/2020/05/Loudya_200520_edita-19052020-12.25.mp3Podcast:[…]

This edition of GARNet Research Roundup begins with two studies from the John Innes Centre. The first takes a detailed look at meiosis in Arabidopsis arenosa and the second introduces a novel mode of auxin perception. The third paper from the Grierson lab in Bristol uses innovative methods to assess root-soil cohesion through study of[…]

Andre Kuhn works with Lars Ostergaard at the John Innes Centre and discusses a recent Elife paper entitled ‘Direct ETTIN-auxin interaction controls chromatin states in gynoecium development‘. We discuss a new paradigm for auxin perception in the control gene expression. http://blog.garnetcommunity.org.uk/wp-content/uploads/2020/04/200420_Kuhn_edit-20042020-13.57.mp3Podcast: Play in new window | DownloadSubscribe: iTunes | Android | RSS

Bethany Eldridge and Tom Denbigh are co-first authors on a recent paper in Communications Biology entitled ‘Micro-scale interactions between Arabidopsis root hairs and soil particles influence soil erosion‘. We discuss the innovative experimental procedures that they designed to measure the interaction of root hairs with their environment! http://blog.garnetcommunity.org.uk/wp-content/uploads/2020/04/2004254_Eldridge_edit-24042020-11.16.mp3Podcast: Play in new window | DownloadSubscribe: iTunes[…]

GARNet conducted a short survey to assess community-interest in an UK-focused webinar series that will highlights the excellence in UK plant science. Approximately 100 respondants were supportive of the idea so we are kicking off the GARNet-Presents Webinar series on May 5th 2020. This series owes a huge debt of thanks to the widely popular[…]

Chris Morgan who works at the John Innes Centre discusses a recent PNAS paper entitled ‘Derived alleles of two axis proteins affect meiotic traits in autotetraploid Arabidopsis arenosa‘. We discuss the technical challenges of this research as well as the difficulties working from home (or not) with a super-resolution microscope! http://blog.garnetcommunity.org.uk/wp-content/uploads/2020/04/Morgan_200417_edit-17042020-14.59.mp3Podcast: Play in new window[…]

The use of automatic image analysis in the biological sciences has increased significantly in recent years, especially with automated image capture and the rise of phenotyping. This online course will help improve your understanding of image analysis methods, and improve your practical skills and ability to apply the techniques to your images. You will explore[…]

This Easter edition of the GARNet Research Roundup begins with research from Aberystwyth University that has developed a system for studying self-incompatability in self-compatible Arabidopsis. Next is an outstanding community-focussed study led from the John Innes Centre that outlines the development of new resources that better enable discovery-led science to be conducted within hexaploid wheat.[…]

Ludi Wang and Maurice Bosch work at Aberystwyth University and talk to the GARNet Community podcast about a recent paper in JXBot entitled ‘New opportunities and insights into Papaver self-incompatibility by imaging engineered Arabidopsis pollen‘. We discuss the challenges of live imaging Arabidopsis pollen tubes growing in liquid media!! http://blog.garnetcommunity.org.uk/wp-content/uploads/2020/04/Bosch_Wang_200406_edit-07042020-08.56.mp3Podcast: Play in new window |[…]